This file contains all data manipulations, analyses, and visualizations used to produce the temperature, calcification, and survival results in Castillo KD, Bove CB, et al. (In Prep). All gene expression data and analyses can be found in this repository on the RT_Host_Sym_GE.R script and the ITS2 analyses can be found in the reciprocal_transplants_ITS2.Rmd file.
Mean +/- SE and distribution across reefs
| reef | Mean | SD | Min | Max | N | SE |
|---|---|---|---|---|---|---|
| Nearshore | 29.1 | 1.66 | 25.5 | 33.3 | 16088 | 0.0130875 |
| Backreef | 28.7 | 1.61 | 24.6 | 32.5 | 16088 | 0.0126933 |
| Forereef | 28.5 | 1.42 | 25.2 | 31.6 | 16088 | 0.0111953 |
Means (monthly, weekly, daily)
Ranges (monthly, weekly, daily)
Figure 2A. Fraction of surviving Siderastrea siderea colonies through time (2011-2015) after reciprocal transplantation with respect to source location and transplanted location. Source location is represented by line type (FR = dashed; BR = solid; NS = dotted) and transplant location is denoted by color (orange = NS [nearshore], green = BR [backreef], and blue = FR [forereef]).
Table S4. Number or corals surviving per year in each transplant location (BR = backreef, FR = forereef, NS = Nearshore).
| Source | Transplant | 2011 | 2012 | 2013 | 2014 | 2015 |
|---|---|---|---|---|---|---|
| BR | BR | 6 | 6 | 6 | 6 | 6 |
| BR | FR | 6 | 6 | 6 | 5 | 5 |
| BR | NS | 6 | 4 | 3 | 3 | 3 |
| FR | BR | 6 | 6 | 6 | 6 | 6 |
| FR | FR | 6 | 6 | 6 | 6 | 6 |
| FR | NS | 6 | 3 | 2 | 2 | 2 |
| NS | BR | 6 | 6 | 6 | 6 | 6 |
| NS | FR | 6 | 6 | 6 | 6 | 6 |
| NS | NS | 6 | 5 | 4 | 4 | 4 |
sur$Source <- fct_relevel(sur$Source, c("FR", "BR", "NS"))
sur$Transplant <- fct_relevel(sur$Transplant, c("FR", "BR", "NS"))
surv.mod <- coxph(sur.r ~ Transplant + Source, data = sur)
Table S5. Statistical assessment of the cox proportional hazards survival model. (A) Type 2 analysis of deviance of the overall effect of transplant and source. (B) Cox proportional hazard model output, with exp(coef) representing the hazard ratio, se(coef) is the standard error, z is the z score, and Pr(>|z|) is the probability that the estimate could be 0.
| LR Chisq | Df | Pr(>Chisq) | |
|---|---|---|---|
| Transplant | 19.831 | 2 | 4.94e-05 |
| Source | 1.622 | 2 | 4.44e-01 |
| coefficient | exp(coef) | se(coef) | z | Pr(>|z|) | |
|---|---|---|---|---|---|
| TransplantBR | -18.88 | 0.00 | 12566.10 | 0.00 | 1.00 |
| TransplantNS | 2.58 | 13.25 | 1.06 | 2.44 | 0.01 |
| SourceBR | -0.17 | 0.85 | 0.71 | -0.23 | 0.81 |
| SourceNS | -1.00 | 0.37 | 0.87 | -1.15 | 0.25 |
| df | AIC | |
|---|---|---|
| Source * Transplant | 10 | -15.05 |
| Source + Transplant | 6 | -8.51 |
| Transplant only | 4 | -7.76 |
| Source only | 4 | -12.34 |
Model:
calc.model <- lm(rate ~ source * trans, data = RT.calc.fin) # selected model
Modeled Mean Calcification Rate and 95% Confidence Interval
Parametric bootstrapped mean and 95% confidence intervals of calcification rates (mg cm-2 day-1) in response to transplant treatment (BR = backreef, FR = forereef, NS = Nearshore).| Treatment | Modeled Mean | Lower 95% CI | Upper 95% CI |
|---|---|---|---|
| BR to BR | 0.68 | 0.52 | 0.85 |
| BR to FR | 0.64 | 0.45 | 0.83 |
| BR to NS | 0.88 | 0.64 | 1.11 |
| FR to BR | 1.00 | 0.83 | 1.16 |
| FR to FR | 0.91 | 0.78 | 1.04 |
| FR to NS | 0.56 | 0.32 | 0.80 |
| NS to BR | 0.74 | 0.58 | 0.91 |
| NS to FR | 0.76 | 0.61 | 0.90 |
| NS to NS | 0.88 | 0.72 | 1.04 |
Figure 2B. Calcification rate (mg cm–2 day–1) averaged over the entire transplant experimental period (2012 – 2015) by transplant location. Source location is represented by color: orange = NS (nearshore), green = BR (backreef), and blue = FR (forereef). Colored bars represent modeled 95% confidence intervals with corresponding raw calcification rates per colony denoted by circles of the same color.
Year calcification Akaike information criterion (AIC) model selection
Model selection for assessment of source and transplant location impacts on Year coral calcification rates was performed using AIC. The model in bold appropriately fit the data and was used for analyses.| df | AIC | |
|---|---|---|
| Source * Transplant * Year | 28 | 6.48 |
| Source + Transplant + Year | 8 | 19.38 |
| Source * Transplant + Year | 12 | 10.25 |
| Source * Year + Transplant | 12 | 24.21 |
| Transplant * Year + Source | 12 | 6.24 |
| Transplant only | 4 | 67.55 |
| Source only | 4 | 61.23 |
| Year only | 4 | 19.68 |
Model:
tp.model <- lm(rate ~ source * trans * TP, data = RT.calc.tp) # selected model
Modeled Mean Calcification Rate and 95% Confidence Interval by Year
Parametric bootstrapped mean and 95% confidence intervals of calcification rates (mg cm-2 day-1) in response to transplant treatment (BR = backreef, FR = forereef, NS = Nearshore) over time.| Treatment | Modeled Mean | Lower 95% CI | Upper 95% CI |
|---|---|---|---|
| BR to BR in 2013 | 0.53 | 0.35 | 0.71 |
| BR to BR in 2014 | 0.61 | 0.43 | 0.79 |
| BR to BR in 2015 | 0.96 | 0.74 | 1.17 |
| BR to FR in 2013 | 0.58 | 0.36 | 0.80 |
| BR to FR in 2014 | 0.41 | 0.18 | 0.63 |
| BR to FR in 2015 | 0.93 | 0.67 | 1.18 |
| BR to NS in 2013 | 0.57 | 0.34 | 0.78 |
| BR to NS in 2014 | 0.62 | 0.32 | 0.93 |
| BR to NS in 2015 | 1.48 | 1.18 | 1.80 |
| FR to BR in 2013 | 0.78 | 0.60 | 0.95 |
| FR to BR in 2014 | 0.83 | 0.65 | 1.01 |
| FR to BR in 2015 | 1.26 | 1.05 | 1.48 |
| FR to FR in 2013 | 0.99 | 0.82 | 1.17 |
| FR to FR in 2014 | 0.70 | 0.53 | 0.88 |
| FR to FR in 2015 | 1.05 | 0.86 | 1.23 |
| FR to NS in 2013 | 0.52 | 0.26 | 0.78 |
| FR to NS in 2014 | 0.25 | -0.06 | 0.57 |
| FR to NS in 2015 | 0.99 | 0.67 | 1.29 |
| NS to BR in 2013 | 0.59 | 0.39 | 0.79 |
| NS to BR in 2014 | 0.76 | 0.57 | 0.96 |
| NS to BR in 2015 | 0.92 | 0.70 | 1.13 |
| NS to FR in 2013 | 0.79 | 0.61 | 0.96 |
| NS to FR in 2014 | 0.67 | 0.49 | 0.86 |
| NS to FR in 2015 | 0.84 | 0.62 | 1.05 |
| NS to NS in 2013 | 0.73 | 0.50 | 0.95 |
| NS to NS in 2014 | 0.59 | 0.38 | 0.80 |
| NS to NS in 2015 | 1.33 | 1.12 | 1.55 |
Figure S2A | Calcification rate (mg cm-2 day-1) at yearly intervals over the entire transplant experimental period (2012 – 2015) by source location. Transplant location is represented by color: red = NS (nearshore), green = BR (backreef), and blue = FR (forereef). Colored bars represent modeled 95% confidence intervals with corresponding raw calcification rates per colony denoted by circles of the same color.
Table S1. Akaike information criterion (AIC) model selection for calcification linear models. Model selection for assessment of source and transplant location impacts on overall (2012 - 2015) and annual coral calcification rates performed using AIC. The model with the lowest AIC (in bold) best fit the data and was used for analyses.
| df | AIC | |
|---|---|---|
| Overall Calcification | ||
| Source * Transplant | 10 | -15.05 |
| Source + Transplant | 6 | -8.51 |
| Transplant only | 4 | -7.76 |
| Source only | 4 | -12.34 |
| Annual Calcification | ||
| Source * Transplant * Year | 28 | 6.48 |
| Source + Transplant + Year | 8 | 19.38 |
| Source * Transplant + Year | 12 | 10.25 |
| Source * Year + Transplant | 12 | 24.21 |
| Transplant * Year + Source | 12 | 6.24 |
| Transplant only | 4 | 67.55 |
| Source only | 4 | 61.23 |
| Year only | 4 | 19.68 |
Table S6 Linear model output assessing overall calcification responses. The intercept was set at corals from the backreef (BR) transplanted back to the backreef.
| Estimate | Std. Error | t value | Pr(>|t|) | |
|---|---|---|---|---|
| (Intercept) | 0.68 | 0.08 | 8.10 | 0.00 |
| source (FR) | 0.32 | 0.12 | 2.65 | 0.01 |
| source (NS) | 0.06 | 0.12 | 0.49 | 0.63 |
| transplant (FR) | -0.05 | 0.13 | -0.37 | 0.72 |
| transplant (NS) | 0.19 | 0.15 | 1.33 | 0.20 |
| source (FR):transplant (FR) | -0.04 | 0.17 | -0.22 | 0.83 |
| source (NS):transplant (FR) | 0.07 | 0.17 | 0.38 | 0.71 |
| source (FR):transplant (NS) | -0.63 | 0.21 | -3.03 | 0.01 |
| source (NS):transplant (NS) | -0.05 | 0.19 | -0.28 | 0.78 |
Table S7. Modeled mean calcification rate and 95% confidence interval. Parametric bootstrapped mean and 95% confidence intervals of calcification rates (mg cm-2 day-1) in response to transplant treatment (BR = backreef, FR = forereef, NS = Nearshore).
| Treatment | Modeled Mean | Lower 95% CI | Upper 95% CI |
|---|---|---|---|
| BR to BR | 0.68 | 0.52 | 0.85 |
| BR to FR | 0.64 | 0.45 | 0.83 |
| BR to NS | 0.88 | 0.64 | 1.11 |
| FR to BR | 1.00 | 0.83 | 1.16 |
| FR to FR | 0.91 | 0.78 | 1.04 |
| FR to NS | 0.56 | 0.32 | 0.80 |
| NS to BR | 0.74 | 0.58 | 0.91 |
| NS to FR | 0.76 | 0.61 | 0.90 |
| NS to NS | 0.88 | 0.72 | 1.04 |
Table S8 Linear model output assessing annual calcification responses. The intercept was set at corals from the backreef (BR) transplanted back to the backreef from 2013.
| Estimate | Std. Error | t value | Pr(>|t|) | |
|---|---|---|---|---|
| (Intercept) | 0.53 | 0.09 | 5.79 | 0.00 |
| source (FR) | 0.25 | 0.13 | 1.94 | 0.06 |
| source (NS) | 0.06 | 0.14 | 0.44 | 0.66 |
| transplant (FR) | 0.05 | 0.14 | 0.34 | 0.74 |
| transplant (NS) | 0.04 | 0.14 | 0.27 | 0.78 |
| Year (2014) | 0.08 | 0.13 | 0.63 | 0.53 |
| Year (2015) | 0.43 | 0.14 | 2.98 | 0.00 |
| source (FR):transplant (FR) | 0.16 | 0.19 | 0.85 | 0.40 |
| source (NS):transplant (FR) | 0.15 | 0.20 | 0.75 | 0.45 |
| source (FR):transplant (NS) | -0.30 | 0.21 | -1.40 | 0.17 |
| source (NS):transplant (NS) | 0.10 | 0.21 | 0.50 | 0.62 |
| source (FR):Year (2014) | -0.03 | 0.18 | -0.17 | 0.87 |
| source (NS):Year (2014) | 0.09 | 0.19 | 0.48 | 0.63 |
| source (FR):Year (2015) | 0.06 | 0.20 | 0.27 | 0.79 |
| source (NS):Year (2015) | -0.09 | 0.21 | -0.44 | 0.66 |
| transplant (FR):Year (2014) | -0.25 | 0.20 | -1.23 | 0.22 |
| transplant (NS):Year (2014) | -0.03 | 0.23 | -0.13 | 0.90 |
| transplant (FR):Year (2015) | -0.08 | 0.22 | -0.36 | 0.72 |
| transplant (NS):Year (2015) | 0.48 | 0.24 | 1.99 | 0.05 |
| source (FR):transplant (FR):Year (2014) | -0.09 | 0.27 | -0.32 | 0.75 |
| source (NS):transplant (FR):Year (2014) | -0.03 | 0.28 | -0.11 | 0.91 |
| source (FR):transplant (NS):Year (2014) | -0.28 | 0.34 | -0.85 | 0.40 |
| source (NS):transplant (NS):Year (2014) | -0.28 | 0.31 | -0.90 | 0.37 |
| source (FR):transplant (FR):Year (2015) | -0.35 | 0.30 | -1.19 | 0.24 |
| source (NS):transplant (FR):Year (2015) | -0.20 | 0.31 | -0.66 | 0.51 |
| source (FR):transplant (NS):Year (2015) | -0.50 | 0.35 | -1.43 | 0.16 |
| source (NS):transplant (NS):Year (2015) | -0.22 | 0.32 | -0.68 | 0.50 |
Table S9. Modeled mean calcification rate and 95% confidence interval by year. Parametric bootstrapped mean and 95% confidence intervals of calcification rates (mg cm-2 day-1) in response to transplant treatment (BR = backreef, FR = forereef, NS = Nearshore) over time.
| Treatment | Modeled Mean | Lower 95% CI | Upper 95% CI |
|---|---|---|---|
| BR to BR in 2013 | 0.53 | 0.35 | 0.71 |
| BR to BR in 2014 | 0.61 | 0.43 | 0.79 |
| BR to BR in 2015 | 0.96 | 0.74 | 1.17 |
| BR to FR in 2013 | 0.58 | 0.36 | 0.80 |
| BR to FR in 2014 | 0.41 | 0.18 | 0.63 |
| BR to FR in 2015 | 0.93 | 0.67 | 1.18 |
| BR to NS in 2013 | 0.57 | 0.34 | 0.78 |
| BR to NS in 2014 | 0.62 | 0.32 | 0.93 |
| BR to NS in 2015 | 1.48 | 1.18 | 1.80 |
| FR to BR in 2013 | 0.78 | 0.60 | 0.95 |
| FR to BR in 2014 | 0.83 | 0.65 | 1.01 |
| FR to BR in 2015 | 1.26 | 1.05 | 1.48 |
| FR to FR in 2013 | 0.99 | 0.82 | 1.17 |
| FR to FR in 2014 | 0.70 | 0.53 | 0.88 |
| FR to FR in 2015 | 1.05 | 0.86 | 1.23 |
| FR to NS in 2013 | 0.52 | 0.26 | 0.78 |
| FR to NS in 2014 | 0.25 | -0.06 | 0.57 |
| FR to NS in 2015 | 0.99 | 0.67 | 1.29 |
| NS to BR in 2013 | 0.59 | 0.39 | 0.79 |
| NS to BR in 2014 | 0.76 | 0.57 | 0.96 |
| NS to BR in 2015 | 0.92 | 0.70 | 1.13 |
| NS to FR in 2013 | 0.79 | 0.61 | 0.96 |
| NS to FR in 2014 | 0.67 | 0.49 | 0.86 |
| NS to FR in 2015 | 0.84 | 0.62 | 1.05 |
| NS to NS in 2013 | 0.73 | 0.50 | 0.95 |
| NS to NS in 2014 | 0.59 | 0.38 | 0.80 |
| NS to NS in 2015 | 1.33 | 1.12 | 1.55 |
(These model outputs are taken from the plasticity analysis and just constructed into tables here)
Table S3. Akaike information criterion (AIC) model selection for coral host and algal symbiont gene expression plasticity. Model selection for assessment of source and transplant location impacts on gene expression plasticity performed using AIC.
| Host Model | AIC | BIC | Nagelkerke’s R2 |
|---|---|---|---|
| Source * Transplant | 46.845 | 64.687 | 0.833 |
| Source + Transplant | 102.088 | 112.794 | 0.146 |
| Transplant | 99.632 | 106.769 | 0.108 |
| Source | 102.398 | 109.535 | 0.034 |
| Symbiont Model | AIC | BIC | Nagelkerke’s R2 |
|---|---|---|---|
| Source * Transplant | 31.742 | 46.714 | 0.863 |
| Source + Transplant | 94.949 | 104.930 | 0.038 |
| Transplant | 91.827 | 98.481 | 0.011 |
| Source | 91.317 | 97.971 | 0.027 |
(These model outputs are taken from the plasticity analysis and just constructed into tables here)
Table S10A. Linear model output assessing coral host gene expression plasticity. The intercept was set at corals from the backreef transplanted back to the backreef. (BR = backreef, FR = forereef, NS = Nearshore)
| Estimate | Std. Error | t value | Pr(>t) | |
|---|---|---|---|---|
| (Intercept) | -0.6692 | 0.1731 | -3.866 | 0.000460 *** |
| Source (FR) | 1.1464 | 0.2448 | 4.683 | 4.17e-05 *** |
| Source (NS) | 0.6369 | 0.2568 | 2.481 | 0.018072 * |
| Transplant (FR) | 1.1503 | 0.2448 | 4.699 | 3.97e-05 *** |
| Transplant (NS) | 0.0778 | 0.2998 | 0.259 | 0.796787 |
| Source (FR):Transplant (FR) | -3.0430 | 0.3462 | -8.789 | 2.22e-10 *** |
| Source (NS):Transplant (FR) | -0.2569 | 0.3548 | -0.724 | 0.473857 |
| Source (FR):Transplant (NS) | 0.1188 | 0.4580 | 0.259 | 0.796844 |
| Source (NS):Transplant (NS) | -1.5480 | 0.4133 | -3.746 | 0.000647 *** |
(These model outputs are taken from the plasticity analysis and just constructed into tables here)
Table S10B. Linear model output assessing algal symbiont gene expression plasticity. The intercept was set at corals from the backreef transplanted back to the backreef. (BR = backreef, FR = forereef, NS = Nearshore)
| Estimate | Std. Error | t value | Pr(>t) | |
|---|---|---|---|---|
| (Intercept) | -1.2588 | 0.1355 | -9.290 | 1.80e-10 *** |
| Source (FR) | 1.7762 | 0.1916 | 9.270 | 1.90e-10 *** |
| Source (NS) | 1.5797 | 0.2142 | 7.374 | 2.66e-08 *** |
| Transplant (FR) | 1.5676 | 0.1916 | 8.181 | 3.06e-09 *** |
| Transplant (NS) | 2.0990 | 0.2347 | 8.944 | 4.29e-10 *** |
| Source (FR):Transplant (FR) | -2.9321 | 0.2710 | -10.820 | 4.72e-12 *** |
| Source (NS):Transplant (FR) | -1.0877 | 0.3030 | -3.590 | 0.00112 ** |
| Source (FR):Transplant (NS) | NA | NA | NA | NA |
| Source (NS):Transplant (NS) | -3.0780 | 0.3319 | -9.274 | 1.88e-10 *** |
Figure 1: Map of reef environments on the southern Belize Mesoamerican Barrier Reef System with in situ seawater temperatures recorded at these locations. (A) Model showing locations of forereef (FR; blue), backreef (BR; green), and nearshore (NS; orange) environments. Forereef and backreef sites are ~2-km apart on the seaward and landward sides of the Barrier Reef’s crest, respectively. The nearshore site is located 30-km west toward mainland Belize. (B) Mean (±1 SD) and distribution of in situ seawater temperatures taken every 30 minutes at forereef (blue), backreef (green), and nearshore (orange) environments from November 2014 to November 2015. (C) Weekly temperature ranges across the three reef environments demonstrating differences in temperature variability across sites.
Figure S1. In situ temperatures recorded every 30 minutes from November 2014 to October 2015 on the nearshore (NS; orange), backreef (BR; green), and forereef (FR; blue) habitats assessed during this reciprocal transplant experiment on the Belize MBRS. (A) Raw temperature observations showing overall temperature patterns through the sampling period at each site. (B) Monthly, (C) Weekly, and (D) daily mean temperature comparisons across the three reef environments. (E) Monthly and (F) daily temperature ranges across the three reef environments demonstrating differences in temperature variability across sites.
Supplemental Figure 2. Calcification rate (mg cm–2 day–1) coloured by either (A-B) transplant or (C) source location (orange = NS [nearshore], green = BR [backreef], and blue = FR [forereef]), at (A, C) yearly intervals or (B) averaged over the entire transplant experimental period. Colored bars represent modeled 95% confidence intervals with corresponding raw calcification rates per colony denoted by circles of the same color.
Last run on 07 August 2023
## R version 3.6.3 (2020-02-29)
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